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<p>A complete telomere-to-telomere (T2T) pig genome serves as a high-precision reference for functional genomics and structural variation studies due to its high level of completeness and minimal error rate. Here we present a comprehensive framework for genomic research aimed at the effective utilization of Neijiang pig genetic resources. The highly repetitive centromeric regions of the Neijiang pig are identified, and their characteristic centromeric landscapes are constructed using chromosomal landmark identification combined with centromeric repeat monomer localization strategies. Genome-wide association studies (GWAS) based on the T2T reference genome identify key genetic loci associated with reproductive traits, offering potential molecular targets for genetic improvement. Gene family analysis and genetic investigation into head morphology in Neijiang pigs reveal selection signals within olfactory receptor (OR) genes that are associated with head shape differentiation, highlighting the potential role of environmental adaptation in the phenotypic domestication of Chinese indigenous pig breeds. The Neijiang pig T2T genome (NJP-T2T) assembly provides a critical reference resource and foundational dataset for genetic improvement and functional genomic studies in indigenous pig breeds.</p>

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The Neijiang pig T2T genome reveals domestication history and germplasm traits of Southwest Chinese local breeds

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年1月16日

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  • Dong Chen,
  • Shengdi Cui,
  • Zhenjian Zhao,
  • Pingxian Wu,
  • Wenxuan Zhou,
  • Patrick Kofi Makafui Tecku,
  • Kai Wang,
  • Junge Wang,
  • Ziyang Chen,
  • Shixin Yu,
  • Jiamiao Chen,
  • Yaoxi Zhou,
  • Runjie Huang,
  • Xuewei Li,
  • Guoqing Tang

摘要

A complete telomere-to-telomere (T2T) pig genome serves as a high-precision reference for functional genomics and structural variation studies due to its high level of completeness and minimal error rate. Here we present a comprehensive framework for genomic research aimed at the effective utilization of Neijiang pig genetic resources. The highly repetitive centromeric regions of the Neijiang pig are identified, and their characteristic centromeric landscapes are constructed using chromosomal landmark identification combined with centromeric repeat monomer localization strategies. Genome-wide association studies (GWAS) based on the T2T reference genome identify key genetic loci associated with reproductive traits, offering potential molecular targets for genetic improvement. Gene family analysis and genetic investigation into head morphology in Neijiang pigs reveal selection signals within olfactory receptor (OR) genes that are associated with head shape differentiation, highlighting the potential role of environmental adaptation in the phenotypic domestication of Chinese indigenous pig breeds. The Neijiang pig T2T genome (NJP-T2T) assembly provides a critical reference resource and foundational dataset for genetic improvement and functional genomic studies in indigenous pig breeds.